Impact of Tandem Repeats on the Scaling of Nucleotide Sequences

Techniques such as detrended fluctuation analysis (DFA) and its extensions have been widely used to determine the nature of scaling in nucleotide sequences. In this brief communication we show that tandem repeats which are ubiquitous in nucleotide sequences can prevent reliable estimation of possible long-range correlations. Therefore, it is important to investigate the presence of tandem repeats prior to scaling exponent estimation.Comment: 14 Pages, 3 Figure

A5_4 Bang Goes that Theory

This paper investigates the plausibility of a handgun firing a bullet due to heating it up on a gas stove, as seen in the 2011 film Final Destination 5. We find that for a firing pin made out of steel it would take a temperature change of 2858.8K to cause the firing pin to expand the 0.2cm. We have also found that this temperature could not be attained by a gas stove.

A5_3 Indiana Jones and the Fridge to Freedom

This paper investigates the plausibility of Indiana Jones being able to survive the initial gamma ray radiation from a nuclear explosion by containing himself within a lead-lined fridge. We find that the fridge needs a thickness of lead to be at least 6.83cm for him to be unharmed by the gamma radiation.

Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts

BACKGROUND: The replication of mammalian genomic DNA during the S phase is a highly coordinated process that occurs in a programmed manner. Recent studies have begun to elucidate the pattern of replication timing on a genomic scale. Using a combination of experimental and computational techniques, we identified a genome-wide set of the earliest replicating sequences. This was accomplished by first creating a cosmid library containing DNA enriched in sequences that replicate early in the S phase of normal human fibroblasts. Clone ends were then sequenced and aligned to the human genome. RESULTS: By clustering adjacent or overlapping early replicating clones, we identified 1759 "islands" averaging 100 kb in length, allowing us to perform the most detailed analysis to date of DNA characteristics and genes contained within early replicating DNA. Islands are enriched in open chromatin, transcription related elements, and Alu repetitive elements, with an underrepresentation of LINE elements. In addition, we found a paucity of LTR retroposons, DNA transposon sequences, and an enrichment in all classes of tandem repeats, except for dinucleotides. CONCLUSION: An analysis of genes associated with islands revealed that nearly half of all genes in the WNT family, and a number of genes in the base excision repair pathway, including four of ten DNA glycosylases, were associated with island sequences. Also, we found an overrepresentation of members of apoptosis-associated genes in very early replicating sequences from both fibroblast and lymphoblastoid cells. These data suggest that there is a temporal pattern of replication for some functionally related genes

L-selectin mediated leukocyte tethering in shear flow is controlled by multiple contacts and cytoskeletal anchorage facilitating fast rebinding events

L-selectin mediated tethers result in leukocyte rolling only above a threshold in shear. Here we present biophysical modeling based on recently published data from flow chamber experiments (Dwir et al., J. Cell Biol. 163: 649-659, 2003) which supports the interpretation that L-selectin mediated tethers below the shear threshold correspond to single L-selectin carbohydrate bonds dissociating on the time scale of milliseconds, whereas L-selectin mediated tethers above the shear threshold are stabilized by multiple bonds and fast rebinding of broken bonds, resulting in tether lifetimes on the timescale of $10^{-1}$ seconds. Our calculations for cluster dissociation suggest that the single molecule rebinding rate is of the order of $10^4$ Hz. A similar estimate results if increased tether dissociation for tail-truncated L-selectin mutants above the shear threshold is modeled as diffusive escape of single receptors from the rebinding region due to increased mobility. Using computer simulations, we show that our model yields first order dissociation kinetics and exponential dependence of tether dissociation rates on shear stress. Our results suggest that multiple contacts, cytoskeletal anchorage of L-selectin and local rebinding of ligand play important roles in L-selectin tether stabilization and progression of tethers into persistent rolling on endothelial surfaces.Comment: 9 pages, Revtex, 4 Postscript figures include

Pulsed laser deposition growth of heteroepitaxial YBa2Cu3O7/La0.67Ca0.33MnO3 superlattices on NdGaO3 and Sr0.7La0.3Al0.65Ta0.35O3 substrates

Heteroepitaxial superlattices of [YBa2Cu3O7(n)/ La0.67Ca0.33MnO3(m)]x, where n and m are the number of YBCO and LCMO monolayers and x the number of bilayer repetitions, have been grown with pulsed laser deposition on NdGaO3 (110) and Sr0.7La0.3Al0.65Ta0.35O3 (LSAT) (001). These substrates are well lattice matched with YBCO and LCMO and, unlike the commonly used SrTiO3, they do not give rise to complex and uncontrolled strain effects due to structural transitions at low temperature. The growth dynamics and the structure have been studied in-situ with reflection high energy electron diffraction (RHEED) and ex-situ with scanning transmission electron microscopy (STEM), x-ray diffraction, and neutron reflectometry. The individual layers are found to be flat and continuous over long lateral distances with sharp and coherent interfaces and with a well-defined thickness of the individual layer. The only visible defects are antiphase boundaries in the YBCO layers that originate from perovskite unit cell height steps at the interfaces with the LCMO layers. We also find that the first YBCO monolayer at the interface with LCMO has an unusual growth dynamics and is lacking the CuO chain layer while the subsequent YBCO layers have the regular Y-123 structure. Accordingly, the CuO2 bilayers at both the LCMO/YBCO and the YBCO/LCMO interfaces are lacking one of their neighboring CuO chain layers and thus half of their hole doping reservoir. Nevertheless, from electric transport measurements on asuperlattice with n=2 we obtain evidence that the interfacial CuO2 bilayers remain conducting and even exhibit the onset of a superconducting transition at very low temperature. Finally, we show from dc magnetization and neutron reflectometry measurements that the LCMO layers are strongly ferromagnetic

Automation and robotics considerations for a lunar base

An envisioned lunar outpost shares with other NASA missions many of the same criteria that have prompted the development of intelligent automation techniques with NASA. Because of increased radiation hazards, crew surface activities will probably be even more restricted than current extravehicular activity in low Earth orbit. Crew availability for routine and repetitive tasks will be at least as limited as that envisioned for the space station, particularly in the early phases of lunar development. Certain tasks are better suited to the untiring watchfulness of computers, such as the monitoring and diagnosis of multiple complex systems, and the perception and analysis of slowly developing faults in such systems. In addition, mounting costs and constrained budgets require that human resource requirements for ground control be minimized. This paper provides a glimpse of certain lunar base tasks as seen through the lens of automation and robotic (A&R) considerations. This can allow a more efficient focusing of research and development not only in A&R, but also in those technologies that will depend on A&R in the lunar environment

In-Space Robotic Assembly Joint Characterization Approach

This paper describes the test systems and approaches developed to characterize the performance of a structural joint that is intended for robotic in-space assembly (ISA). The design of the joint is based on a heritage concept from National Aeronautics and Space Administration (NASA) Langley Research Center (LaRC) originally intended for structural assembly by astronauts during extravehicular activity (EVA). Its design was modified under a public-private partnership and is intended to accelerate the availability of, and reduce costs for the infusion of NASA developed technologies into commercial ISA systems. Test systems were developed to measure the axial, bending, and torsional stiffness of the joint at a wide range of temperatures. A test system was also developed to measure the reliability of the joint in terms of translation and rotation when disassembled and re-assembled in space. These test systems were used to characterize the joint behavior and provide performance data for the iterative joint design process. The paper also lists the lessons learned to aid testing of next generation robotic in-space assembly joints

Bacterial profiling reveals novel "Ca. Neoehrlichia", Ehrlichia, and anaplasma species in Australian human-biting ticks

In Australia, a conclusive aetiology of Lyme disease-like illness in human patients remains elusive, despite growing numbers of people presenting with symptoms attributed to tick bites. In the present study, we surveyed the microbial communities harboured by human-biting ticks from across Australia to identify bacteria that may contribute to this syndrome. Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes in DNA samples from individual Ixodes holocyclus (n = 279), Amblyomma triguttatum (n = 167), Haemaphysalis bancrofti (n = 7), and H. longicornis (n = 7) ticks. The 16S amplicons were sequenced on the Illumina MiSeq platform and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomies. Nested PCR and Sanger sequencing were used to confirm the NGS data and further analyse novel findings. All 460 ticks were negative for Borrelia spp. by both NGS and nested PCR analysis. Two novel “Candidatus Neoehrlichia” spp. were identified in 12.9% of I. holocyclus ticks. A novel Anaplasma sp. was identified in 1.8% of A. triguttatum ticks, and a novel Ehrlichia sp. was identified in both A. triguttatum (1.2%) ticks and a single I. holocyclus (0.6%) tick. Further phylogenetic analysis of novel “Ca. Neoehrlichia”, Anaplasma and Ehrlichia based on 1,265 bp 16S rRNA gene sequences suggests that these are new species. Determining whether these newly discovered organisms cause disease in humans and animals, like closely related bacteria do abroad, is of public health importance and requires further investigation